Starting phenix.real_space_refine on Mon Jun 9 13:54:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xk4_38415/06_2025/8xk4_38415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xk4_38415/06_2025/8xk4_38415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xk4_38415/06_2025/8xk4_38415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xk4_38415/06_2025/8xk4_38415.map" model { file = "/net/cci-nas-00/data/ceres_data/8xk4_38415/06_2025/8xk4_38415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xk4_38415/06_2025/8xk4_38415.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5734 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 3 7.51 5 P 22 5.49 5 S 29 5.16 5 C 3791 2.51 5 N 1075 2.21 5 O 1128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6048 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5589 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 665} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 255 Classifications: {'DNA': 12} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 11} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 179 Classifications: {'DNA': 9} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {' MN': 1} Classifications: {'DNA': 1, 'undetermined': 1} Modifications used: {'p5*END': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.41, per 1000 atoms: 0.73 Number of scatterers: 6048 At special positions: 0 Unit cell: (75.739, 89.355, 110.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 3 24.99 S 29 16.00 P 22 15.00 O 1128 8.00 N 1075 7.00 C 3791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 824.0 milliseconds 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1312 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 33.4% alpha, 19.9% beta 8 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 85 through 105 removed outlier: 3.538A pdb=" N ARG A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.654A pdb=" N MET A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 288 removed outlier: 3.704A pdb=" N TRP A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 removed outlier: 4.200A pdb=" N GLY A 329 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.583A pdb=" N ILE A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.807A pdb=" N LYS A 387 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 388 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 389 " --> pdb=" O THR A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 394 through 400 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 432 through 442 removed outlier: 3.505A pdb=" N GLY A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 removed outlier: 3.666A pdb=" N ILE A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 Processing helix chain 'A' and resid 491 through 508 removed outlier: 4.115A pdb=" N THR A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 585 Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.552A pdb=" N VAL A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'A' and resid 681 through 693 removed outlier: 3.622A pdb=" N SER A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 721 removed outlier: 3.639A pdb=" N ARG A 721 " --> pdb=" O THR A 717 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 13 removed outlier: 5.151A pdb=" N ILE A 144 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 127 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A 122 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE A 129 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLN A 120 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU A 131 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.785A pdb=" N VAL A 23 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU A 74 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 187 Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 232 removed outlier: 4.065A pdb=" N ILE A 231 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR A 242 " --> pdb=" O ILE A 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.618A pdb=" N THR A 646 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N CYS A 522 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N HIS A 594 " --> pdb=" O CYS A 522 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE A 524 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASP A 596 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE A 526 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 382 removed outlier: 6.584A pdb=" N VAL A 417 " --> pdb=" O GLN A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 528 through 531 removed outlier: 4.571A pdb=" N SER A 535 " --> pdb=" O LEU A 559 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 609 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1617 1.33 - 1.45: 1195 1.45 - 1.57: 3312 1.57 - 1.69: 45 1.69 - 1.81: 51 Bond restraints: 6220 Sorted by residual: bond pdb=" P DC B 102 " pdb=" OP3 DC B 102 " ideal model delta sigma weight residual 1.480 1.606 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" P DT C 7 " pdb=" OP3 DT C 7 " ideal model delta sigma weight residual 1.480 1.606 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 1.480 1.600 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" N SER A 611 " pdb=" CA SER A 611 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.82e+00 bond pdb=" CA SER A 611 " pdb=" CB SER A 611 " ideal model delta sigma weight residual 1.528 1.490 0.039 1.59e-02 3.96e+03 5.89e+00 ... (remaining 6215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 8267 1.61 - 3.22: 188 3.22 - 4.83: 29 4.83 - 6.44: 11 6.44 - 8.05: 4 Bond angle restraints: 8499 Sorted by residual: angle pdb=" N PRO A 474 " pdb=" CA PRO A 474 " pdb=" CB PRO A 474 " ideal model delta sigma weight residual 103.25 111.30 -8.05 1.05e+00 9.07e-01 5.87e+01 angle pdb=" C PHE A 319 " pdb=" N HIS A 320 " pdb=" CA HIS A 320 " ideal model delta sigma weight residual 121.54 129.53 -7.99 1.91e+00 2.74e-01 1.75e+01 angle pdb=" N SER A 611 " pdb=" CA SER A 611 " pdb=" C SER A 611 " ideal model delta sigma weight residual 111.36 107.17 4.19 1.09e+00 8.42e-01 1.48e+01 angle pdb=" N ILE A 268 " pdb=" CA ILE A 268 " pdb=" C ILE A 268 " ideal model delta sigma weight residual 113.20 109.53 3.67 9.60e-01 1.09e+00 1.46e+01 angle pdb=" N VAL A 264 " pdb=" CA VAL A 264 " pdb=" C VAL A 264 " ideal model delta sigma weight residual 113.07 107.90 5.17 1.36e+00 5.41e-01 1.44e+01 ... (remaining 8494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.68: 3463 27.68 - 55.35: 160 55.35 - 83.03: 13 83.03 - 110.71: 3 110.71 - 138.38: 1 Dihedral angle restraints: 3640 sinusoidal: 1612 harmonic: 2028 Sorted by residual: dihedral pdb=" CA LYS A 77 " pdb=" C LYS A 77 " pdb=" N ARG A 78 " pdb=" CA ARG A 78 " ideal model delta harmonic sigma weight residual -180.00 -156.88 -23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA LEU A 270 " pdb=" C LEU A 270 " pdb=" N SER A 271 " pdb=" CA SER A 271 " ideal model delta harmonic sigma weight residual -180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ILE A 374 " pdb=" C ILE A 374 " pdb=" N ALA A 375 " pdb=" CA ALA A 375 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 3637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 919 0.107 - 0.213: 25 0.213 - 0.320: 1 0.320 - 0.426: 0 0.426 - 0.533: 2 Chirality restraints: 947 Sorted by residual: chirality pdb=" P DT C 7 " pdb=" OP1 DT C 7 " pdb=" OP2 DT C 7 " pdb=" O5' DT C 7 " both_signs ideal model delta sigma weight residual True 2.35 2.88 -0.53 2.00e-01 2.50e+01 7.10e+00 chirality pdb=" P DC B 102 " pdb=" OP1 DC B 102 " pdb=" OP2 DC B 102 " pdb=" O5' DC B 102 " both_signs ideal model delta sigma weight residual True 2.35 -2.84 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" P DT B 1 " pdb=" OP1 DT B 1 " pdb=" OP2 DT B 1 " pdb=" O5' DT B 1 " both_signs ideal model delta sigma weight residual True 2.35 2.61 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 944 not shown) Planarity restraints: 1002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 257 " 0.064 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO A 258 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT B 1 " 0.032 2.00e-02 2.50e+03 1.62e-02 6.60e+00 pdb=" N1 DT B 1 " -0.035 2.00e-02 2.50e+03 pdb=" C2 DT B 1 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DT B 1 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DT B 1 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT B 1 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT B 1 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DT B 1 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT B 1 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DT B 1 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 510 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 511 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " -0.022 5.00e-02 4.00e+02 ... (remaining 999 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 18 2.38 - 3.01: 2986 3.01 - 3.64: 8479 3.64 - 4.27: 13700 4.27 - 4.90: 23035 Nonbonded interactions: 48218 Sorted by model distance: nonbonded pdb=" OP2 DT C 7 " pdb="MN MN C 101 " model vdw 1.749 2.320 nonbonded pdb=" O VAL A 737 " pdb="MN MN B 101 " model vdw 1.761 2.320 nonbonded pdb=" OP1 DT B 1 " pdb="MN MN B 101 " model vdw 1.807 2.320 nonbonded pdb=" OD1 ASP A 713 " pdb="MN MN C 101 " model vdw 1.941 2.320 nonbonded pdb=" OP1 DA B 3 " pdb="MN MN B 101 " model vdw 2.096 2.320 ... (remaining 48213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.580 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 6220 Z= 0.206 Angle : 0.634 8.046 8499 Z= 0.370 Chirality : 0.050 0.533 947 Planarity : 0.005 0.095 1002 Dihedral : 15.225 138.384 2328 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.67 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.32), residues: 681 helix: -0.48 (0.37), residues: 203 sheet: 0.78 (0.45), residues: 146 loop : -1.52 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 43 HIS 0.007 0.001 HIS A 612 PHE 0.024 0.001 PHE A 319 TYR 0.018 0.001 TYR A 352 ARG 0.003 0.000 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.19063 ( 239) hydrogen bonds : angle 7.20322 ( 647) covalent geometry : bond 0.00432 ( 6220) covalent geometry : angle 0.63390 ( 8499) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.632 Fit side-chains REVERT: A 56 HIS cc_start: 0.7119 (m-70) cc_final: 0.6586 (m170) REVERT: A 310 ASP cc_start: 0.6192 (m-30) cc_final: 0.5751 (m-30) REVERT: A 539 MET cc_start: 0.7246 (mpp) cc_final: 0.6890 (mmt) REVERT: A 639 THR cc_start: 0.8538 (m) cc_final: 0.8309 (p) outliers start: 0 outliers final: 1 residues processed: 133 average time/residue: 1.1101 time to fit residues: 155.6224 Evaluate side-chains 88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 183 GLN A 259 GLN A 461 GLN A 548 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.188925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151326 restraints weight = 6108.436| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.71 r_work: 0.3452 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6220 Z= 0.131 Angle : 0.539 6.473 8499 Z= 0.299 Chirality : 0.043 0.169 947 Planarity : 0.004 0.054 1002 Dihedral : 12.887 139.674 978 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.99 % Allowed : 12.58 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.32), residues: 681 helix: -0.10 (0.37), residues: 218 sheet: 1.04 (0.46), residues: 143 loop : -1.42 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 282 HIS 0.005 0.001 HIS A 590 PHE 0.023 0.001 PHE A 351 TYR 0.018 0.001 TYR A 37 ARG 0.007 0.000 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 239) hydrogen bonds : angle 4.82422 ( 647) covalent geometry : bond 0.00307 ( 6220) covalent geometry : angle 0.53886 ( 8499) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.664 Fit side-chains REVERT: A 56 HIS cc_start: 0.7714 (m-70) cc_final: 0.7220 (m170) REVERT: A 310 ASP cc_start: 0.6758 (m-30) cc_final: 0.6422 (m-30) REVERT: A 371 LYS cc_start: 0.8140 (tppt) cc_final: 0.7834 (mmmt) REVERT: A 539 MET cc_start: 0.8001 (mpp) cc_final: 0.7712 (mmt) outliers start: 12 outliers final: 3 residues processed: 107 average time/residue: 0.9676 time to fit residues: 109.8223 Evaluate side-chains 89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 424 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 2 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 120 GLN A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.180445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.142224 restraints weight = 6229.763| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.85 r_work: 0.3370 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6220 Z= 0.188 Angle : 0.593 7.001 8499 Z= 0.325 Chirality : 0.045 0.178 947 Planarity : 0.005 0.045 1002 Dihedral : 13.252 138.581 978 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.81 % Allowed : 14.40 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.32), residues: 681 helix: -0.24 (0.35), residues: 221 sheet: 1.03 (0.46), residues: 137 loop : -1.59 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 282 HIS 0.006 0.001 HIS A 320 PHE 0.021 0.002 PHE A 319 TYR 0.018 0.001 TYR A 37 ARG 0.005 0.000 ARG A 275 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 239) hydrogen bonds : angle 4.83714 ( 647) covalent geometry : bond 0.00454 ( 6220) covalent geometry : angle 0.59252 ( 8499) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.597 Fit side-chains REVERT: A 310 ASP cc_start: 0.6963 (m-30) cc_final: 0.6637 (m-30) REVERT: A 371 LYS cc_start: 0.8172 (tppt) cc_final: 0.7874 (mmmt) REVERT: A 432 ARG cc_start: 0.6521 (mtm-85) cc_final: 0.6224 (mtp85) REVERT: A 643 ARG cc_start: 0.7632 (ttm-80) cc_final: 0.7186 (mtt180) REVERT: A 678 LYS cc_start: 0.8116 (pmmt) cc_final: 0.7410 (tppt) REVERT: A 719 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.7629 (t80) outliers start: 23 outliers final: 8 residues processed: 98 average time/residue: 0.9606 time to fit residues: 99.9406 Evaluate side-chains 89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 259 GLN A 289 GLN A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.183355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.147775 restraints weight = 6287.206| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.64 r_work: 0.3413 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6220 Z= 0.130 Angle : 0.518 5.844 8499 Z= 0.286 Chirality : 0.042 0.148 947 Planarity : 0.004 0.042 1002 Dihedral : 12.990 137.241 976 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.15 % Allowed : 16.23 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.32), residues: 681 helix: 0.04 (0.36), residues: 220 sheet: 1.17 (0.46), residues: 137 loop : -1.47 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.006 0.001 HIS A 320 PHE 0.016 0.001 PHE A 319 TYR 0.014 0.001 TYR A 37 ARG 0.004 0.000 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 239) hydrogen bonds : angle 4.58300 ( 647) covalent geometry : bond 0.00301 ( 6220) covalent geometry : angle 0.51783 ( 8499) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.613 Fit side-chains REVERT: A 310 ASP cc_start: 0.6925 (m-30) cc_final: 0.6601 (m-30) REVERT: A 371 LYS cc_start: 0.8220 (tppt) cc_final: 0.7971 (mmmt) REVERT: A 432 ARG cc_start: 0.6423 (mtm-85) cc_final: 0.6188 (mtp85) REVERT: A 540 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7765 (tpp) REVERT: A 643 ARG cc_start: 0.7592 (ttm-80) cc_final: 0.7132 (mtt180) REVERT: A 678 LYS cc_start: 0.8102 (pmmt) cc_final: 0.7451 (tppt) REVERT: A 689 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7863 (p) outliers start: 19 outliers final: 4 residues processed: 95 average time/residue: 0.9219 time to fit residues: 93.1736 Evaluate side-chains 85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 689 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 63 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 289 GLN A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.178540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140011 restraints weight = 6262.770| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.81 r_work: 0.3411 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6220 Z= 0.152 Angle : 0.546 5.908 8499 Z= 0.299 Chirality : 0.043 0.145 947 Planarity : 0.004 0.043 1002 Dihedral : 13.051 137.999 976 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.98 % Allowed : 17.22 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.32), residues: 681 helix: -0.05 (0.35), residues: 222 sheet: 1.17 (0.46), residues: 137 loop : -1.50 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 282 HIS 0.004 0.001 HIS A 710 PHE 0.019 0.001 PHE A 319 TYR 0.014 0.001 TYR A 37 ARG 0.006 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 239) hydrogen bonds : angle 4.72159 ( 647) covalent geometry : bond 0.00359 ( 6220) covalent geometry : angle 0.54636 ( 8499) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.593 Fit side-chains REVERT: A 310 ASP cc_start: 0.6963 (m-30) cc_final: 0.6616 (m-30) REVERT: A 371 LYS cc_start: 0.8110 (tppt) cc_final: 0.7877 (mmmt) REVERT: A 432 ARG cc_start: 0.6467 (mtm-85) cc_final: 0.6267 (mtp85) REVERT: A 540 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7836 (tpp) REVERT: A 608 LYS cc_start: 0.7936 (tppp) cc_final: 0.7678 (ttpt) REVERT: A 643 ARG cc_start: 0.7664 (ttm-80) cc_final: 0.7207 (mtt180) REVERT: A 678 LYS cc_start: 0.8124 (pmmt) cc_final: 0.7488 (tppt) REVERT: A 719 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7643 (t80) outliers start: 18 outliers final: 8 residues processed: 92 average time/residue: 0.9007 time to fit residues: 88.3523 Evaluate side-chains 86 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 chunk 49 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.185461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150960 restraints weight = 6117.219| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.77 r_work: 0.3456 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6220 Z= 0.124 Angle : 0.509 5.748 8499 Z= 0.280 Chirality : 0.043 0.225 947 Planarity : 0.004 0.041 1002 Dihedral : 12.930 137.123 976 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.32 % Allowed : 18.54 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.32), residues: 681 helix: 0.05 (0.36), residues: 224 sheet: 1.25 (0.46), residues: 137 loop : -1.42 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 512 HIS 0.003 0.001 HIS A 710 PHE 0.015 0.001 PHE A 319 TYR 0.014 0.001 TYR A 37 ARG 0.004 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 239) hydrogen bonds : angle 4.58554 ( 647) covalent geometry : bond 0.00286 ( 6220) covalent geometry : angle 0.50882 ( 8499) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.599 Fit side-chains REVERT: A 310 ASP cc_start: 0.6964 (m-30) cc_final: 0.6619 (m-30) REVERT: A 371 LYS cc_start: 0.8097 (tppt) cc_final: 0.7893 (mmmt) REVERT: A 432 ARG cc_start: 0.6544 (mtm-85) cc_final: 0.6336 (mtp85) REVERT: A 540 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7821 (tpp) REVERT: A 608 LYS cc_start: 0.7819 (tppp) cc_final: 0.7551 (ttpt) REVERT: A 643 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7277 (mtt180) REVERT: A 678 LYS cc_start: 0.8132 (pmmt) cc_final: 0.7493 (tppt) REVERT: A 689 VAL cc_start: 0.8140 (OUTLIER) cc_final: 0.7889 (p) REVERT: A 719 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7634 (t80) outliers start: 14 outliers final: 6 residues processed: 91 average time/residue: 0.9687 time to fit residues: 93.6366 Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 44 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.180016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143136 restraints weight = 6208.076| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.84 r_work: 0.3387 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6220 Z= 0.132 Angle : 0.526 6.019 8499 Z= 0.287 Chirality : 0.043 0.212 947 Planarity : 0.004 0.043 1002 Dihedral : 12.927 137.532 976 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.81 % Allowed : 19.21 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.32), residues: 681 helix: 0.18 (0.36), residues: 222 sheet: 1.27 (0.46), residues: 137 loop : -1.40 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 512 HIS 0.003 0.001 HIS A 710 PHE 0.016 0.001 PHE A 319 TYR 0.014 0.001 TYR A 37 ARG 0.007 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 239) hydrogen bonds : angle 4.55935 ( 647) covalent geometry : bond 0.00309 ( 6220) covalent geometry : angle 0.52618 ( 8499) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.577 Fit side-chains REVERT: A 133 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8329 (tt) REVERT: A 310 ASP cc_start: 0.7067 (m-30) cc_final: 0.6703 (m-30) REVERT: A 371 LYS cc_start: 0.8067 (tppt) cc_final: 0.7837 (mmmt) REVERT: A 432 ARG cc_start: 0.6614 (mtm-85) cc_final: 0.6337 (mtp85) REVERT: A 540 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7773 (tpp) REVERT: A 608 LYS cc_start: 0.7813 (tppp) cc_final: 0.7522 (ttpt) REVERT: A 643 ARG cc_start: 0.7655 (ttm-80) cc_final: 0.7196 (mtt180) REVERT: A 678 LYS cc_start: 0.8108 (pmmt) cc_final: 0.7469 (tppt) REVERT: A 719 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7617 (t80) outliers start: 17 outliers final: 7 residues processed: 92 average time/residue: 0.8836 time to fit residues: 86.5519 Evaluate side-chains 85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.179198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139540 restraints weight = 6183.294| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.92 r_work: 0.3369 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6220 Z= 0.147 Angle : 0.543 5.841 8499 Z= 0.295 Chirality : 0.043 0.207 947 Planarity : 0.004 0.045 1002 Dihedral : 12.976 137.895 976 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.98 % Allowed : 19.87 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.32), residues: 681 helix: 0.14 (0.36), residues: 222 sheet: 1.19 (0.46), residues: 143 loop : -1.33 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 512 HIS 0.004 0.001 HIS A 710 PHE 0.018 0.001 PHE A 319 TYR 0.013 0.001 TYR A 37 ARG 0.004 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 239) hydrogen bonds : angle 4.64081 ( 647) covalent geometry : bond 0.00346 ( 6220) covalent geometry : angle 0.54314 ( 8499) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.863 Fit side-chains REVERT: A 142 ASN cc_start: 0.5729 (OUTLIER) cc_final: 0.5139 (t0) REVERT: A 310 ASP cc_start: 0.7063 (m-30) cc_final: 0.6697 (m-30) REVERT: A 371 LYS cc_start: 0.8011 (tppt) cc_final: 0.7768 (mmmt) REVERT: A 432 ARG cc_start: 0.6609 (mtm-85) cc_final: 0.6347 (mtp85) REVERT: A 540 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7804 (tpp) REVERT: A 608 LYS cc_start: 0.7818 (tppp) cc_final: 0.7523 (ttpt) REVERT: A 643 ARG cc_start: 0.7680 (ttm-80) cc_final: 0.7232 (mtt180) REVERT: A 678 LYS cc_start: 0.8099 (pmmt) cc_final: 0.7476 (tppt) REVERT: A 719 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7574 (t80) outliers start: 18 outliers final: 8 residues processed: 94 average time/residue: 1.0606 time to fit residues: 107.0980 Evaluate side-chains 88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.180904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143044 restraints weight = 6215.721| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.79 r_work: 0.3450 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6220 Z= 0.128 Angle : 0.528 6.708 8499 Z= 0.288 Chirality : 0.042 0.201 947 Planarity : 0.004 0.045 1002 Dihedral : 12.897 137.302 976 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.48 % Allowed : 20.20 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.32), residues: 681 helix: 0.24 (0.36), residues: 222 sheet: 1.16 (0.45), residues: 143 loop : -1.26 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 512 HIS 0.003 0.001 HIS A 710 PHE 0.016 0.001 PHE A 319 TYR 0.013 0.001 TYR A 37 ARG 0.008 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 239) hydrogen bonds : angle 4.51473 ( 647) covalent geometry : bond 0.00297 ( 6220) covalent geometry : angle 0.52755 ( 8499) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.661 Fit side-chains REVERT: A 133 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8329 (tt) REVERT: A 142 ASN cc_start: 0.5526 (OUTLIER) cc_final: 0.5222 (t0) REVERT: A 310 ASP cc_start: 0.7014 (m-30) cc_final: 0.6663 (m-30) REVERT: A 432 ARG cc_start: 0.6634 (mtm-85) cc_final: 0.6391 (mtp85) REVERT: A 540 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7805 (tpp) REVERT: A 608 LYS cc_start: 0.7808 (tppp) cc_final: 0.7560 (ttpt) REVERT: A 643 ARG cc_start: 0.7675 (ttm-80) cc_final: 0.7250 (mtt180) REVERT: A 678 LYS cc_start: 0.8097 (pmmt) cc_final: 0.7507 (tppt) REVERT: A 689 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7969 (p) REVERT: A 719 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.7619 (t80) outliers start: 15 outliers final: 6 residues processed: 94 average time/residue: 1.0607 time to fit residues: 106.2956 Evaluate side-chains 90 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 33 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.178995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.139377 restraints weight = 6274.265| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.92 r_work: 0.3391 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6220 Z= 0.150 Angle : 0.548 6.373 8499 Z= 0.298 Chirality : 0.043 0.209 947 Planarity : 0.004 0.045 1002 Dihedral : 12.988 138.158 976 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.99 % Allowed : 21.03 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.32), residues: 681 helix: 0.15 (0.35), residues: 222 sheet: 1.10 (0.45), residues: 143 loop : -1.28 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 512 HIS 0.004 0.001 HIS A 710 PHE 0.019 0.001 PHE A 319 TYR 0.015 0.001 TYR A 37 ARG 0.003 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 239) hydrogen bonds : angle 4.61116 ( 647) covalent geometry : bond 0.00352 ( 6220) covalent geometry : angle 0.54818 ( 8499) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.785 Fit side-chains REVERT: A 289 GLN cc_start: 0.8241 (mm-40) cc_final: 0.8027 (mt0) REVERT: A 310 ASP cc_start: 0.7028 (m-30) cc_final: 0.6662 (m-30) REVERT: A 432 ARG cc_start: 0.6625 (mtm-85) cc_final: 0.6352 (mtp85) REVERT: A 540 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7810 (tpp) REVERT: A 608 LYS cc_start: 0.7843 (tppp) cc_final: 0.7547 (ttpt) REVERT: A 643 ARG cc_start: 0.7700 (ttm-80) cc_final: 0.7270 (mtt180) REVERT: A 678 LYS cc_start: 0.8097 (pmmt) cc_final: 0.7471 (tppt) REVERT: A 719 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.7673 (t80) outliers start: 12 outliers final: 7 residues processed: 88 average time/residue: 1.1221 time to fit residues: 105.7123 Evaluate side-chains 85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 719 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.181914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.143919 restraints weight = 6271.292| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.74 r_work: 0.3384 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6220 Z= 0.152 Angle : 0.556 10.066 8499 Z= 0.300 Chirality : 0.044 0.206 947 Planarity : 0.004 0.048 1002 Dihedral : 13.007 138.402 976 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.15 % Allowed : 21.03 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.32), residues: 681 helix: 0.04 (0.35), residues: 227 sheet: 1.11 (0.45), residues: 143 loop : -1.30 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 512 HIS 0.004 0.001 HIS A 710 PHE 0.020 0.002 PHE A 319 TYR 0.014 0.001 TYR A 37 ARG 0.006 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 239) hydrogen bonds : angle 4.60744 ( 647) covalent geometry : bond 0.00357 ( 6220) covalent geometry : angle 0.55558 ( 8499) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5024.09 seconds wall clock time: 89 minutes 2.61 seconds (5342.61 seconds total)